RNAinteract (version 1.20.0)

plotDoublePerturbation: Double Perturbation Plot

Description

These function draws a double perturbation plot for interaction screens. All interactions of one gene are displayed in one panel. The double perturbation readout level is plotted against the single perturbation level.

Usage

plotDoublePerturbation( sgi, screen, channel, target, withoutgroups = c("neg", "pos"), design, main, xlab, ylab, range, show.labels = "none", label.par, label,
		       avoid.overlap, col, fill, D , MT, MQ, PV, QV, PI, ...)

Arguments

sgi

An object of class RNAinteract.

target

A character name of the target gene.

screen

The character name of the screen to display. If not specified, the first screen is used. Does not have to be specified, if sgi contains only one screen.

channel

The character name of the channel to display. If not specified, the first channel is used. Does not have to be specified, if sgi contains only one channel.

withoutgroups

Interactions to genes from these groups (as specified in the reagent or target annotation) are excluded from the plot, e.g. positive and negative controls.

design

The Either "template" (default) or "query". The single perturbation effects are either the template main effects or the query main effects.

main

An overall title of the plot.

xlab

A title of the x-axis.

ylab

A title of the y-axis.

range

A numeric vector of length two. range equals the xlim, ylim argument in plot.

show.labels

Automatically select text labels for the points. 'all' shows a text label for all genes, "q.value" and "p.value" show a text label for all genes with a q.value (p.value) larger than label.par, "none" does not show any text label. This argument has no effect, if label is specified.

label.par

Cut-off value for q.value or p.value for displaying text labels (See show.labels).

label

Either a character vector with gene names, or a named vector of text labels. The names of the vector represent the gene names.

avoid.overlap

If TRUE (default), text is moved such that text labels are not overlapping.

col

A named vector with colors. The names of col define which points are colored (See also fill).

fill

A list up to four values. colors defines a set of colors from which a colorramp is created. If colramp is specified, colors has no effect. colramp directly specifies the colorramp. values define the values that are color coded. If values is not specified, the pairwise interaction term is used instead. at is a numeric vector defining the breakpoints along the values. If not specified, breakpoints are selected to range three times the standard deviation of the values around zero. fill has no effect, if col is specified.

D,MT,MQ,PV,QV,PI

Internal usage.

...

Further argument passed to grid.doublePerturbation or doublePerturbationGrob.

Value

A grob is returned.

Details

Plots a double perturbation plot. It shows the interaction profile for one (query) gene.

See Also

RNAinteract-package, grid.doublePerturbation, reportDoublePerturbation

Examples

data("sgi")
plotDoublePerturbation( sgi, screen="1", channel="nrCells", target="rl", show.labels="p.value")